Reading quadrature encoder using Riox

The Riox 1216AHRS datasheet mentions there are 3 quadrature encoder inputs on the Riox and in the riox configuration utility, in the In/Out tab there are 3 counters which I imagine are for this. My question is how should the pins be configured for quadrature encoder inputs? There does not seem to be an option for this in the operating mode of the pulse I/Os. Any help would be greatly appreciated.

Its been a while since I've asked this question but I'm yet to find an answer. I have tried the commands in the motor controller user guide for setting a pulse pin as a counter (PINA) and to assign a pulse pin to a motor (PMOD) but this didn't work. If anyone can point me in the right direction or confirm if this functionality has been implemented that would be great

I got the following reply from roboteq in case anyone else is interested in doing this:
Yes, the RIOX supports up to 3 incremental encoders. The connections are as below:
Encoder pin   Riox pin
1A    1
1B    2
2A    3
2B    4
3A    5
3B    6

To make them work you need to make sure the in Pulse Inputs 1-6, the operating mode is set to “Disabled”. Then you need to send the following command to activate the encoders:
 
^emod x y         with x = encoder 1 or 2 or 3 and y = 0 for off and 1 for on.
 
For example,
 
^emod 1 1          will activate the encoder 1
^emod 3 0          will deactivate the encoder 3
 
Then you need to save this with the command
 
%eesav
 
And the setting will be retained to the memory.